allele [GENO_0000512]

One of a set of sequence features known to exist at a particular genomic location. An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a ‘gene allele’ that spans the extent of an entire gene which contains several sequence alterations). Alleles can carry ‘reference’ or ‘variant’ sequence - depending on whether the its ‘state’ matches that considered to be the reference at that location. Alleles whose state differs from the reference are called ‘variant alleles’, and those that match the reference are called ‘reference alleles’. What is considered the ‘reference’ state at a particular location may vary, depending on the context/goal of a particular analysis. A ‘sequence alteration’ is a ‘variant allele’ that varies along its entire extent (i.e every position varies from that of some defined reference sequence).
Tags:

Open allele in VFB

VFB Term Json

{
    "term": {
        "core": {
            "iri": "http://purl.obolibrary.org/obo/GENO_0000512",
            "symbol": "",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "GENO_0000512",
            "label": "allele"
        },
        "description": [
            "One of a set of sequence features known to exist at a particular genomic location."
        ],
        "comment": [
            "An allele is a seqeunce feature at a genomic location where variation occurs (i.e. where >1 different sequence is known to exist). An allele can span only the extent of sequence known to vary (e.g. a single base SNP, or short insertion), or it can span a larger extent that includes one or more variable features as proper parts (e.g. a 'gene allele' that spans the extent of an entire gene which contains several sequence alterations).\n\nAlleles can carry 'reference' or 'variant' sequence - depending on whether the its 'state' matches that considered to be the reference at that location. Alleles whose state differs from the reference are called 'variant alleles', and those that match the reference are called 'reference alleles'. What is considered the 'reference' state at a particular location may vary, depending on the context/goal of a particular analysis. A 'sequence alteration' is a 'variant allele' that varies along its entire extent (i.e every position varies from that of some defined reference sequence)."
        ]
    },
    "query": "Get JSON for Class",
    "version": "44725ae",
    "parents": [
        {
            "symbol": "",
            "iri": "http://purl.obolibrary.org/obo/GENO_0000481",
            "types": [
                "Entity",
                "Class"
            ],
            "short_form": "GENO_0000481",
            "label": "genomic feature"
        }
    ],
    "relationships": [
        {
            "relation": {
                "iri": "http://purl.obolibrary.org/obo/GENO_0000683",
                "label": "varies_with",
                "type": "varies_with"
            },
            "object": {
                "symbol": "",
                "iri": "http://purl.obolibrary.org/obo/GENO_0000481",
                "types": [
                    "Entity",
                    "Class"
                ],
                "short_form": "GENO_0000481",
                "label": "genomic feature"
            }
        }
    ],
    "xrefs": [],
    "anatomy_channel_image": [],
    "pub_syn": [],
    "def_pubs": [
        {
            "core": {
                "symbol": "",
                "iri": "http://flybase.org/reports/Unattributed",
                "types": [
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                    "Individual",
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                "short_form": "Unattributed",
                "label": ""
            },
            "FlyBase": "",
            "PubMed": "",
            "DOI": ""
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}